5 research outputs found
The ancient evolutionary history of polyomaviruses
Author Summary: Polyomaviruses are a family of DNA-based viruses that are known to infect various terrestrial vertebrates, including humans. In this report, we describe our discovery of highly divergent polyomaviruses associated with various marine fish. Searches of public deep sequencing databases unexpectedly revealed the existence of polyomavirus-like sequences in scorpion and spider datasets. Our analysis of these new sequences suggests that polyomaviruses have slowly co-evolved with individual host animal lineages through an established mechanism known as intrahost divergence. The proposed model is similar to the mechanisms through with other DNA viruses, such as papillomaviruses, are thought to have evolved. Our analysis also suggests that distantly related polyomaviruses sometimes recombine to produce new chimeric lineages. We propose a possible taxonomic scheme that can account for these inferred ancient recombination events
Genetic diversity of human sapovirus across the Americas
Background: Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. Objective/study design: To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US). Results: VP1 genotyping showed that all sapovirus sequences could be grouped in the four established genogroups (GI (n = 13), GII (n = 30), GIV (n = 23), GV (n = 2)) that infect humans. They include the near-complete genome of a GI.6 virus and a recently reported novel GII.8 virus. Sequences of the complete RNA-dependent RNA polymerase gene could be grouped into three major genetic clusters or polymerase (P) types (GI.P, GII.P and GV.P) with all GIV viruses harboring a GII polymerase. One (GII.P-GII.4) of the new 68 sequences was a recombinant virus with the hotspot between the NS7 and VP1 regions. Conclusions: Analyses of this expanded database of near-complete sapovirus sequences showed several mismatches in the genotyping primers, suggesting opportunities to revisit and update current sapovirus typing methods
Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch
Viruses preserved in ancient materials provide snapshots of past
viral diversity and a means to trace viral evolution through time.
Here, we use a metagenomics approach to identify filterable and
nuclease-resistant nucleic acids preserved in 700-y-old caribou
feces frozen in a permanent ice patch. We were able to recover
and characterize two viruses in replicated experiments performed
in two different laboratories: a small circular DNA viral genome
(ancient caribou feces associated virus, or aCFV) and a partial RNA
viral genome (Ancient Northwest Territories cripavirus, or aNCV).
Phylogenetic analysis identifies aCFV as distantly related to the
plant-infecting geminiviruses and the fungi-infecting Sclerotinia
sclerotiorum hypovirulence-associated DNA virus 1 and aNCV as
within the insect-infecting Cripavirus genus. We hypothesize that
these viruses originate from plant material ingested by caribou or
from flying insects and that their preservation can be attributed to
protection within viral capsids maintained at cold temperatures.
To investigate the tropism of aCFV, we used the geminiviral reverse
genetic system and introduced a multimeric clone into the
laboratory model plant Nicotiana benthamiana. Evidence for infectivity
came from the detection of viral DNA in newly emerged
leaves and the precise excision of the viral genome from the multimeric
clones in inoculated leaves. Our findings indicate that viral
genomes may in some circumstances be protected from degradation
for centuries
Taxonomy of the order Mononegavirales: update 2018
In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future